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Protocol for structural and biochemical analyses of RhoA GTPase.

STAR protocols

Lin Y, Watanabe-Chailland M, Zheng Y.
PMID: 34036285
STAR Protoc. 2021 May 14;2(2):100541. doi: 10.1016/j.xpro.2021.100541. eCollection 2021 Jun 18.

Ras GTPases in complex with Guanosine triphosphate (GTP) or GTP analog exhibit dynamic equilibrium between two interconvertible conformations-an inactive state 1 and an active state 2. Unlike Ras, it remains unclear if the GTP-bound form of Rho GTPases also...

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Lin Y, Watanabe-Chailland M, Zheng Y. Protocol for structural and biochemical analyses of RhoA GTPase. STAR Protoc. 2021;2(2):100541doi: 10.1016/j.xpro.2021.100541.
Lin, Y., Watanabe-Chailland, M., & Zheng, Y. (2021). Protocol for structural and biochemical analyses of RhoA GTPase. STAR protocols, 2(2), 100541. https://doi.org/10.1016/j.xpro.2021.100541
Lin, Yuan, et al. "Protocol for structural and biochemical analyses of RhoA GTPase." STAR protocols vol. 2,2 (2021): 100541. doi: https://doi.org/10.1016/j.xpro.2021.100541
Lin Y, Watanabe-Chailland M, Zheng Y. Protocol for structural and biochemical analyses of RhoA GTPase. STAR Protoc. 2021 May 14;2(2):100541. doi: 10.1016/j.xpro.2021.100541. eCollection 2021 Jun 18. PMID: 34036285; PMCID: PMC8138865.
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Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling.

Chemistry (Weinheim an der Bergstrasse, Germany)

Marín-Ramos NI, Piñar C, Vázquez-Villa H, Martín-Fontecha M, González Á, Canales Á, Algar S, Mayo PP, Jiménez-Barbero J, Gajate C, Mollinedo F, Pardo L, Ortega-Gutiérrez S, Viso A, López-Rodríguez ML.
PMID: 27885731
Chemistry. 2017 Jan 31;23(7):1676-1685. doi: 10.1002/chem.201604905. Epub 2016 Dec 27.

Despite more than three decades of intense effort, no anti-Ras therapies have reached clinical application. Contributing to this failure has been an underestimation of Ras complexity and a dearth of structural information. In this regard, recent studies have revealed...

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Marín-Ramos NI, Piñar C, Vázquez-Villa H, et al. Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry. 2016;23(7):1676-1685doi: 10.1002/chem.201604905.
Marín-Ramos, N. I., Piñar, C., Vázquez-Villa, H., Martín-Fontecha, M., González, �. �., Canales, �. �., Algar, S., Mayo, P. P., Jiménez-Barbero, J., Gajate, C., Mollinedo, F., Pardo, L., Ortega-Gutiérrez, S., Viso, A., & López-Rodríguez, M. L. (2017). Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry (Weinheim an der Bergstrasse, Germany), 23(7), 1676-1685. https://doi.org/10.1002/chem.201604905
Marín-Ramos, Nagore I, et al. "Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling." Chemistry (Weinheim an der Bergstrasse, Germany) vol. 23,7 (2017): 1676-1685. doi: https://doi.org/10.1002/chem.201604905
Marín-Ramos NI, Piñar C, Vázquez-Villa H, Martín-Fontecha M, González Á, Canales Á, Algar S, Mayo PP, Jiménez-Barbero J, Gajate C, Mollinedo F, Pardo L, Ortega-Gutiérrez S, Viso A, López-Rodríguez ML. Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry. 2017 Jan 31;23(7):1676-1685. doi: 10.1002/chem.201604905. Epub 2016 Dec 27. PMID: 27885731.
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Ribavirin suppresses hepatic lipogenesis through inosine monophosphate dehydrogenase inhibition: Involvement of adenosine monophosphate-activated protein kinase-related kinases and retinoid X receptor α.

Hepatology communications

Satoh S, Mori K, Onomura D, Ueda Y, Dansako H, Honda M, Kaneko S, Ikeda M, Kato N.
PMID: 29404478
Hepatol Commun. 2017 Jul 13;1(6):550-563. doi: 10.1002/hep4.1065. eCollection 2017 Aug.

Ribavirin (RBV) has been widely used as an antiviral reagent, specifically for patients with chronic hepatitis C. We previously demonstrated that adenosine kinase, which monophosphorylates RBV into the metabolically active form, is a key determinant for RBV sensitivity against...

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Satoh S, Mori K, Onomura D, et al. Ribavirin suppresses hepatic lipogenesis through inosine monophosphate dehydrogenase inhibition: Involvement of adenosine monophosphate-activated protein kinase-related kinases and retinoid X receptor α. Hepatol Commun. 2017;1(6):550-563doi: 10.1002/hep4.1065.
Satoh, S., Mori, K., Onomura, D., Ueda, Y., Dansako, H., Honda, M., Kaneko, S., Ikeda, M., & Kato, N. (2017). Ribavirin suppresses hepatic lipogenesis through inosine monophosphate dehydrogenase inhibition: Involvement of adenosine monophosphate-activated protein kinase-related kinases and retinoid X receptor α. Hepatology communications, 1(6), 550-563. https://doi.org/10.1002/hep4.1065
Satoh, Shinya, et al. "Ribavirin suppresses hepatic lipogenesis through inosine monophosphate dehydrogenase inhibition: Involvement of adenosine monophosphate-activated protein kinase-related kinases and retinoid X receptor α." Hepatology communications vol. 1,6 (2017): 550-563. doi: https://doi.org/10.1002/hep4.1065
Satoh S, Mori K, Onomura D, Ueda Y, Dansako H, Honda M, Kaneko S, Ikeda M, Kato N. Ribavirin suppresses hepatic lipogenesis through inosine monophosphate dehydrogenase inhibition: Involvement of adenosine monophosphate-activated protein kinase-related kinases and retinoid X receptor α. Hepatol Commun. 2017 Jul 13;1(6):550-563. doi: 10.1002/hep4.1065. eCollection 2017 Aug. PMID: 29404478; PMCID: PMC5678905.
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Rho GTPases in Skeletal Muscle Development and Homeostasis.

Cells

Rodríguez-Fdez S, Bustelo XR.
PMID: 34831205
Cells. 2021 Nov 02;10(11). doi: 10.3390/cells10112984.

Rho guanosine triphosphate hydrolases (GTPases) are molecular switches that cycle between an inactive guanosine diphosphate (GDP)-bound and an active guanosine triphosphate (GTP)-bound state during signal transduction. As such, they regulate a wide range of both cellular and physiological processes....

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Rodríguez-Fdez S, Bustelo XR. Rho GTPases in Skeletal Muscle Development and Homeostasis. Cells. 2021;10(11)doi: 10.3390/cells10112984.
Rodríguez-Fdez, S., & Bustelo, X. R. (2021). Rho GTPases in Skeletal Muscle Development and Homeostasis. Cells, 10(11), . https://doi.org/10.3390/cells10112984
Rodríguez-Fdez, Sonia, and Bustelo, Xosé R. "Rho GTPases in Skeletal Muscle Development and Homeostasis." Cells vol. 10,11 (2021). doi: https://doi.org/10.3390/cells10112984
Rodríguez-Fdez S, Bustelo XR. Rho GTPases in Skeletal Muscle Development and Homeostasis. Cells. 2021 Nov 02;10(11). doi: 10.3390/cells10112984. PMID: 34831205; PMCID: PMC8616218.
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Role of BAG3 in bovine Deltapapillomavirus-mediated autophagy.

Journal of cellular biochemistry

Roperto S.
PMID: 34889472
J Cell Biochem. 2021 Dec 10; doi: 10.1002/jcb.30193. Epub 2021 Dec 10.

Bovine Deltapapillomavirus genus (δPV), comprises four members that are highly pathogenic and are frequently associated with bladder tumors of adult cattle and water buffaloes. In particular, bovine δPV-2 and δPV-13 are commonly found in urinary bladder tumors in adult...

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Roperto S. Role of BAG3 in bovine Deltapapillomavirus-mediated autophagy. J Cell Biochem. 2021;doi: 10.1002/jcb.30193.
Roperto, S. (2021). Role of BAG3 in bovine Deltapapillomavirus-mediated autophagy. Journal of cellular biochemistry, . https://doi.org/10.1002/jcb.30193
Roperto, Sante. "Role of BAG3 in bovine Deltapapillomavirus-mediated autophagy." Journal of cellular biochemistry vol. (2021). doi: https://doi.org/10.1002/jcb.30193
Roperto S. Role of BAG3 in bovine Deltapapillomavirus-mediated autophagy. J Cell Biochem. 2021 Dec 10; doi: 10.1002/jcb.30193. Epub 2021 Dec 10. PMID: 34889472.
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Chemical capping improves template switching and enhances sequencing of small RNAs.

Nucleic acids research

Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, Sun Z, Guan S, Corrêa IR.
PMID: 34581823
Nucleic Acids Res. 2022 Jan 11;50(1):e2. doi: 10.1093/nar/gkab861.

Template-switching reverse transcription is widely used in RNA sequencing for low-input and low-quality samples, including RNA from single cells or formalin-fixed paraffin-embedded (FFPE) tissues. Previously, we identified the native eukaryotic mRNA 5' cap as a key structural element for...

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Wulf MG, Maguire S, Dai N, et al. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Res. 2022;50(1):e2doi: 10.1093/nar/gkab861.
Wulf, M. G., Maguire, S., Dai, N., Blondel, A., Posfai, D., Krishnan, K., Sun, Z., Guan, S., & Corrêa, I. R. (2022). Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic acids research, 50(1), e2. https://doi.org/10.1093/nar/gkab861
Wulf, Madalee G, et al. "Chemical capping improves template switching and enhances sequencing of small RNAs." Nucleic acids research vol. 50,1 (2022): e2. doi: https://doi.org/10.1093/nar/gkab861
Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, Sun Z, Guan S, Corrêa IR. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Res. 2022 Jan 11;50(1):e2. doi: 10.1093/nar/gkab861. PMID: 34581823.
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Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma.

Journal of the National Cancer Institute

Hadrava Vanova K, Pang Y, Krobova L, Kraus M, Nahacka Z, Boukalova S, Pack SD, Zobalova R, Zhu J, Huynh TT, Jochmanova I, Uher O, Hubackova S, Dvorakova S, Garrett TJ, Ghayee HK, Wu X, Schuster B, Knapp PE, Frysak Z, Hartmann I, Nilubol N, Cerny J, Taieb D, Rohlena J, Neuzil J, Yang C, Pacak K.
PMID: 34415331
J Natl Cancer Inst. 2022 Jan 11;114(1):130-138. doi: 10.1093/jnci/djab158.

BACKGROUND: Pheochromocytoma and paraganglioma (PPGL) are neuroendocrine tumors with frequent mutations in genes linked to the tricarboxylic acid cycle. However, no pathogenic variant has been found to date in succinyl-CoA ligase (SUCL), an enzyme that provides substrate for succinate...

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Hadrava Vanova K, Pang Y, Krobova L, et al. Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma. J Natl Cancer Inst. 2022;114(1):130-138doi: 10.1093/jnci/djab158.
Hadrava Vanova, K., Pang, Y., Krobova, L., Kraus, M., Nahacka, Z., Boukalova, S., Pack, S. D., Zobalova, R., Zhu, J., Huynh, T. T., Jochmanova, I., Uher, O., Hubackova, S., Dvorakova, S., Garrett, T. J., Ghayee, H. K., Wu, X., Schuster, B., Knapp, P. E., Frysak, Z., Hartmann, I., Nilubol, N., Cerny, J., Taieb, D., Rohlena, J., Neuzil, J., Yang, C., & Pacak, K. (2022). Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma. Journal of the National Cancer Institute, 114(1), 130-138. https://doi.org/10.1093/jnci/djab158
Hadrava Vanova, Katerina, et al. "Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma." Journal of the National Cancer Institute vol. 114,1 (2022): 130-138. doi: https://doi.org/10.1093/jnci/djab158
Hadrava Vanova K, Pang Y, Krobova L, Kraus M, Nahacka Z, Boukalova S, Pack SD, Zobalova R, Zhu J, Huynh TT, Jochmanova I, Uher O, Hubackova S, Dvorakova S, Garrett TJ, Ghayee HK, Wu X, Schuster B, Knapp PE, Frysak Z, Hartmann I, Nilubol N, Cerny J, Taieb D, Rohlena J, Neuzil J, Yang C, Pacak K. Germline SUCLG2 Variants in Patients With Pheochromocytoma and Paraganglioma. J Natl Cancer Inst. 2022 Jan 11;114(1):130-138. doi: 10.1093/jnci/djab158. PMID: 34415331.
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In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis.

Computers in biology and medicine

Gerber M, Goel S, Maitra R.
PMID: 34920161
Comput Biol Med. 2021 Dec 09;141:105110. doi: 10.1016/j.compbiomed.2021.105110. Epub 2021 Dec 09.

KRAS mutation is prevalent in around 30% of all cancers and is an undruggable molecular target. Of seven mutations at codon 12 and 13, only one, the G12C mutant is finally proven to be druggable, as evidenced by the...

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Gerber M, Goel S, Maitra R. In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Comput Biol Med. 2021;141:105110doi: 10.1016/j.compbiomed.2021.105110.
Gerber, M., Goel, S., & Maitra, R. (2021). In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Computers in biology and medicine, 141105110. https://doi.org/10.1016/j.compbiomed.2021.105110
Gerber, Michael, et al. "In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis." Computers in biology and medicine vol. 141 (2021): 105110. doi: https://doi.org/10.1016/j.compbiomed.2021.105110
Gerber M, Goel S, Maitra R. In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Comput Biol Med. 2021 Dec 09;141:105110. doi: 10.1016/j.compbiomed.2021.105110. Epub 2021 Dec 09. PMID: 34920161.
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In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis.

Computers in biology and medicine

Gerber M, Goel S, Maitra R.
PMID: 34920161
Comput Biol Med. 2021 Dec 09;141:105110. doi: 10.1016/j.compbiomed.2021.105110. Epub 2021 Dec 09.

KRAS mutation is prevalent in around 30% of all cancers and is an undruggable molecular target. Of seven mutations at codon 12 and 13, only one, the G12C mutant is finally proven to be druggable, as evidenced by the...

Cite
Gerber M, Goel S, Maitra R. In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Comput Biol Med. 2021;141:105110doi: 10.1016/j.compbiomed.2021.105110.
Gerber, M., Goel, S., & Maitra, R. (2021). In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Computers in biology and medicine, 141105110. https://doi.org/10.1016/j.compbiomed.2021.105110
Gerber, Michael, et al. "In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis." Computers in biology and medicine vol. 141 (2021): 105110. doi: https://doi.org/10.1016/j.compbiomed.2021.105110
Gerber M, Goel S, Maitra R. In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis. Comput Biol Med. 2021 Dec 09;141:105110. doi: 10.1016/j.compbiomed.2021.105110. Epub 2021 Dec 09. PMID: 34920161.
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Distinct signaling by insulin and IGF-1 receptors and their extra- and intracellular domains.

Proceedings of the National Academy of Sciences of the United States of America

Nagao H, Cai W, Wewer Albrechtsen NJ, Steger M, Batista TM, Pan H, Dreyfuss JM, Mann M, Kahn CR.
PMID: 33879610
Proc Natl Acad Sci U S A. 2021 Apr 27;118(17). doi: 10.1073/pnas.2019474118.

Insulin and insulin-like growth factor 1 (IGF-1) receptors share many downstream signaling pathways but have unique biological effects. To define the molecular signals contributing to these distinct activities, we performed global phosphoproteomics on cells expressing either insulin receptor (IR),...

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Nagao H, Cai W, Wewer Albrechtsen NJ, et al. Distinct signaling by insulin and IGF-1 receptors and their extra- and intracellular domains. Proc Natl Acad Sci U S A. 2021;118(17)doi: 10.1073/pnas.2019474118.
Nagao, H., Cai, W., Wewer Albrechtsen, N. J., Steger, M., Batista, T. M., Pan, H., Dreyfuss, J. M., Mann, M., & Kahn, C. R. (2021). Distinct signaling by insulin and IGF-1 receptors and their extra- and intracellular domains. Proceedings of the National Academy of Sciences of the United States of America, 118(17), . https://doi.org/10.1073/pnas.2019474118
Nagao, Hirofumi, et al. "Distinct signaling by insulin and IGF-1 receptors and their extra- and intracellular domains." Proceedings of the National Academy of Sciences of the United States of America vol. 118,17 (2021). doi: https://doi.org/10.1073/pnas.2019474118
Nagao H, Cai W, Wewer Albrechtsen NJ, Steger M, Batista TM, Pan H, Dreyfuss JM, Mann M, Kahn CR. Distinct signaling by insulin and IGF-1 receptors and their extra- and intracellular domains. Proc Natl Acad Sci U S A. 2021 Apr 27;118(17). doi: 10.1073/pnas.2019474118. PMID: 33879610; PMCID: PMC8092608.
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Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells.

Science advances

Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC.
PMID: 33962942
Sci Adv. 2021 May 07;7(19). doi: 10.1126/sciadv.abe8349. Print 2021 May.

The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of guanosine triphosphate nucleotides. Among posttranslational modifications initiated at the ER level, glycosylation is the most common reaction. However,...

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Kerselidou D, Dohai BS, Nelson DR, et al. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Sci Adv. 2021;7(19)doi: 10.1126/sciadv.abe8349.
Kerselidou, D., Dohai, B. S., Nelson, D. R., Daakour, S., De Cock, N., Hassoun, Z. A. O., Kim, D. K., Olivet, J., El Assal, D. C., Jaiswal, A., Alzahmi, A., Saha, D., Pain, C., Matthijssens, F., Lemaitre, P., Herfs, M., Chapuis, J., Ghesquiere, B., Vertommen, D., Kriechbaumer, V., Knoops, K., Lopez-Iglesias, C., van Zandvoort, M., Lambert, J. C., Hanson, J., Desmet, C., Thiry, M., Lauersen, K. J., Vidal, M., Van Vlierberghe, P., Dequiedt, F., Salehi-Ashtiani, K., & Twizere, J. C. (2021). Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Science advances, 7(19), . https://doi.org/10.1126/sciadv.abe8349
Kerselidou, Despoina, et al. "Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells." Science advances vol. 7,19 (2021). doi: https://doi.org/10.1126/sciadv.abe8349
Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. Sci Adv. 2021 May 07;7(19). doi: 10.1126/sciadv.abe8349. Print 2021 May. PMID: 33962942; PMCID: PMC8104865.
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Relationship between guanosine triphosphate pathway and tetrahydrobiopterin in gestational diabetes mellitus.

Journal of diabetes and metabolic disorders

Ünüvar S, Melekoğlu R, Şalva E, Acar C, Yaşar Ş.
PMID: 33520842
J Diabetes Metab Disord. 2020 Oct 13;19(2):1391-1396. doi: 10.1007/s40200-020-00659-1. eCollection 2020 Dec.

PURPOSE: The present study assesses the change in tetrahydrobiopterin (BH4), one of the most important products in the guanosine triphosphate (GTP) pathway and in other parameters that might affect nitric oxide (NO) production, in gestational diabetes mellitus (GDM).METHODS: The...

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Ünüvar S, Melekoğlu R, Şalva E, et al. Relationship between guanosine triphosphate pathway and tetrahydrobiopterin in gestational diabetes mellitus. J Diabetes Metab Disord. 2020;19(2):1391-1396doi: 10.1007/s40200-020-00659-1.
Ünüvar, S., Melekoğlu, R., Şalva, E., Acar, C., & Yaşar, �. �. (2020). Relationship between guanosine triphosphate pathway and tetrahydrobiopterin in gestational diabetes mellitus. Journal of diabetes and metabolic disorders, 19(2), 1391-1396. https://doi.org/10.1007/s40200-020-00659-1
Ünüvar, Songül, et al. "Relationship between guanosine triphosphate pathway and tetrahydrobiopterin in gestational diabetes mellitus." Journal of diabetes and metabolic disorders vol. 19,2 (2020): 1391-1396. doi: https://doi.org/10.1007/s40200-020-00659-1
Ünüvar S, Melekoğlu R, Şalva E, Acar C, Yaşar Ş. Relationship between guanosine triphosphate pathway and tetrahydrobiopterin in gestational diabetes mellitus. J Diabetes Metab Disord. 2020 Oct 13;19(2):1391-1396. doi: 10.1007/s40200-020-00659-1. eCollection 2020 Dec. PMID: 33520842; PMCID: PMC7843814.
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